This is a pretty big question! Let's deal with it in parts.
Both characters are caught in a lie. John Proctor is caught in the lie of adultery. Joe Keller is caught in the lie concerning the shipment of defective plane parts.
Both characters have wives who know the truth. They keep their silence and do not speak out but then encourage their husbands to reveal the truth.
Because of these lies, both marriages are filled with tension.
Both characters are leaders...men who are outspoken and do not hold back in their judgements and thoughts.
Both men are concerned about the honor of their name. Joe Keller feels that his name and his business is all that he has to pass on to his son. John Proctor feels that his name, dirty or clean, is all that he has to pass on to his children as well.
Both choose to die in the end in an attempt to restore their dignity and the dignity of their families. John Proctor takes back his confession and hangs with the others. His wife does not stop him because, in her words, "he has his goodness now". Joe Keller comes to realize at the end of the play that "in a way, they were all my sons" and he goes inside to shoot himself. That is his s way of restoring justice and removing the burden from his family.
Proctor dies at the hands of a corrupt justice system where it is next to impossible to prove your innocence. He dies because of his wrongful conviction for witchcraft. Joe Keller dies at his own hands rather than go to the authorities and subject himself to the police and the courts. Keller most likely would have been given prison time, not a death sentence, but his name would have been destroyed in the process.
You could argue that Proctor's death is more noble and his situation more sympathetic than that of Joe Keller. Proctor fought for justice and for the lives of his neighbors and friends. Joe Keller's actions were selfish and motivated by self preservation and greed.
Both families are left fatherless. However, Proctor's family is left with a father who died a hero with his honor and dignity intact. Keller's is left with the memory of a man who hid from the truth to the very end. He died as a coward who would rather commit suicide than face the consequences of his crime. He left his family behind to clean up the mess--both literally and figuratively.